Trends in KEEN Point Count Data

What species are in the swath data?

SP_CODE	SPECIES
AGCL	Agarum clathratum
ALES	Alaria esculenta
ANSP	Anomia
APPA	Aplidium pallidum
ASDI	Ascophyllum nodosum
BLD	UNID Juv Laminariales
BOHA	Bonnemaisonia hamifera
BOSC	Botryllus schlosseri
BOVI	Botrylloides violaceus
BUSP	Bugulina spicata
BUTU	Crisularia turrita
CF	Crepidula fornicata
CHCR	Chondrus crispus
CIIN	Ciona intestinalis
CISA	Ciona savignyi
CLCI	Clathromorphum circumscriptum
CLSP	Cliona
CO	Corallina officinalis
COF	Codium fragile
COPE	Colpomenia peregrina
COTR	Coccotylus truncatus
CREB	Crisia eburnea
CRSP	Ceramium
CYPU	Cystoclonium purpureum
DEAC	Desmarestia aculeata
DECA	Dendrodoa carnea
DEMU	Dendrobeania murrayana
DEVI	Desmarestia viridis
DIAL	Didemnum albidum
DIAT	Diatom Tube Mat
DIP	Diplosoma listerianum
DIVE	Didemnum vexillum
DUCO	Dumontia contorta
EC	Encrusting coralline
EUCR	Euthora cristata
FG	Filamentous Green
HADU	Halisarca dujardinii
HAPA	Halichondria (Halichondria) panicea
HATO	Halosiphon tomentosus
HIRU	Hildenbrandia rubra
HJ	Dasysiphonia japonica
HYSP	Hymedesmia
ISAL	Stenosemus albus
ISRU	Boreochiton ruber
LADI	Laminaria digitata
LESP	Leptophytum acervatum
LEUC	Leucosolenia
LIGL	Lithothamnion
LISP	Lithophyllum
LIVE	Patinella verrucaria
MAST	Mastocarpus stellatus
MEMA	Membranipora membranacea
MOMO	Modiolus modiolus
MYED	Mytilus edulis
OBSP	Obelia
OSED	Ostrea edulis
PAPA	Palmaria palmata
PHRU	Phycodrys rubens
PHSP	Phymatolithon
POLS	Polysiphonia
PORO	Polyides rotunda
PORS	Porphyra
PTSE	Ptilota serrata
RAT	Red Algal Turf
SADE	Saccorhiza dermatodea
SCUN	Schizoporella unicornis
SE	Thylacodes
SL	Saccharina latissima
SLJ	Saccharina latissima
SPRE	Spermothamnion repens
TETE	Testudinalia testudinalis
TISP	Titanoderma
TRIN	Tricellaria inopinata
TUV	Tubular Ulvoid
UEC	Unidentified Erect Coralline
UFR	Unidentified Filamentous Red
URB	Unidentified Red Blade
UV	Blady Ulvoid

Let’s Plot Trends

Here are some functions we’ll apply to each species. I’ll then fit mixed models with all of them using

COUNT ~ YEAR * SITE + (1|TRANSECT)

with a gaussian error. Note, it’s count, so, I could use Poisson, but, that needs to be way more tuned to each model - this should be fine for a first cut?

Here’s how we’ll do it:

tseries_plot <- function(adf){
  
  ggplot(adf,
         aes(y = PERCENT_COVER, x = YEAR,
             color = TRANSECT)) +
    geom_point() +
    geom_line() +
    facet_wrap(~SITE, nrow = 2) +
    labs(color = "Transect", 
         y = "Percent Cover",  x = "Year",
         title = adf$SPECIES[1])
}

tseries_fun <- function(adf){
  glmmTMB(PERCENT_COVER/100+0.001 ~ YEAR * SITE,
               data = adf,
               family = beta_family())
  
}

generate_output <- function(adf){
  cat(paste0("## ", adf$SP_CODE[1], " ", adf$SPECIES[1], "  \n<br>"))
  
  tseries_plot(adf) %>% print()

  if(sum(adf$PERCENT_COVER>10) > 15){
  tseries_fun(adf) %>%
    car::Anova(test.statistic  = "Chisq") %>%
    tidy() %>%
    knitr::kable("html", digits = 3) %>%
    kableExtra::kable_styling() %>%
    print
  }
  
  cat("\n\n")
}

Now let’s purrr::walk() through the whole shebang.

walk(split(upc, upc$SP_CODE), generate_output)

AGCL Agarum clathratum

ALES Alaria esculenta

ANSP Anomia

APPA Aplidium pallidum

ASDI Ascophyllum nodosum

BLD UNID Juv Laminariales

BOHA Bonnemaisonia hamifera

BOSC Botryllus schlosseri

BOVI Botrylloides violaceus

BUSP Bugulina spicata

BUTU Crisularia turrita

CF Crepidula fornicata

## Registered S3 methods overwritten by 'car':
##   method                          from
##   influence.merMod                lme4
##   cooks.distance.influence.merMod lme4
##   dfbeta.influence.merMod         lme4
##   dfbetas.influence.merMod        lme4

term	statistic	df	p.value
YEAR	100307.541	1	0
SITE	2158.400	2	0
YEAR:SITE	2269.389	2	0

CHCR Chondrus crispus

term	statistic	df	p.value
YEAR	54575.43	1	0
SITE	15435.08	2	0
YEAR:SITE	14959.07	2	0

CIIN Ciona intestinalis

CISA Ciona savignyi

CLCI Clathromorphum circumscriptum

CLSP Cliona

CO Corallina officinalis

term	statistic	df	p.value
YEAR	19046.305	1	0
SITE	6465.974	2	0
YEAR:SITE	6235.354	2	0

COF Codium fragile

COPE Colpomenia peregrina

COTR Coccotylus truncatus

CREB Crisia eburnea

CRSP Ceramium

CYPU Cystoclonium purpureum

DEAC Desmarestia aculeata

DECA Dendrodoa carnea

DEMU Dendrobeania murrayana

DEVI Desmarestia viridis

DIAL Didemnum albidum

DIAT Diatom Tube Mat

DIP Diplosoma listerianum

DIVE Didemnum vexillum

DUCO Dumontia contorta

EC Encrusting coralline

EUCR Euthora cristata

FG Filamentous Green

HADU Halisarca dujardinii

HAPA Halichondria (Halichondria) panicea

HATO Halosiphon tomentosus

HIRU Hildenbrandia rubra

HJ Dasysiphonia japonica

term	statistic	df	p.value
YEAR	31440.697	1	0
SITE	1835.231	2	0
YEAR:SITE	1830.743	2	0

HYSP Hymedesmia

ISAL Stenosemus albus

ISRU Boreochiton ruber

LADI Laminaria digitata

LESP Leptophytum acervatum

LEUC Leucosolenia

LIGL Lithothamnion

LISP Lithophyllum

LIVE Patinella verrucaria

MAST Mastocarpus stellatus

MEMA Membranipora membranacea

MOMO Modiolus modiolus

MYED Mytilus edulis

OBSP Obelia

OSED Ostrea edulis

PAPA Palmaria palmata

PHRU Phycodrys rubens

PHSP Phymatolithon

POLS Polysiphonia

term	statistic	df	p.value
YEAR	1277.926	1	0
SITE	43350.015	2	0
YEAR:SITE	42899.533	2	0

PORO Polyides rotunda

PORS Porphyra

PTSE Ptilota serrata

RAT Red Algal Turf

SADE Saccorhiza dermatodea

SCUN Schizoporella unicornis

SE Thylacodes

SL Saccharina latissima

term	statistic	df	p.value
YEAR	5505.378	1	0
SITE	207.203	2	0
YEAR:SITE	193.902	2	0

SLJ Saccharina latissima

SPRE Spermothamnion repens

TETE Testudinalia testudinalis

TISP Titanoderma

TRIN Tricellaria inopinata

TUV Tubular Ulvoid

UEC Unidentified Erect Coralline

UFR Unidentified Filamentous Red

URB Unidentified Red Blade

UV Blady Ulvoid